com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian Maven / Gradle / Ivy
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package com.actelion.research.chem.phesa.pharmacophore.pp;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.PeriodicTable;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.alignment3d.transformation.Transformation;
import com.actelion.research.chem.alignment3d.transformation.TransformationSequence;
import com.actelion.research.chem.phesa.EncodeFunctions;
import com.actelion.research.chem.phesa.Gaussian3D;
import com.actelion.research.chem.phesa.MolecularVolume;
import java.util.Base64;
import java.util.Base64.Decoder;
import java.util.Base64.Encoder;
/**
* @version: 1.0, February 2018
* Author: J. Wahl
* basic class to describe Gaussian functions used for the calculation of Molecular Volumes
* Gaussian functions have a center (3D coordinates), a width and a height
* this class provides functionalities for calculating higher order overlaps of Gaussians
*/
public class PPGaussian extends Gaussian3D {
IPharmacophorePoint pp;
public PPGaussian(int atomicNo,IPharmacophorePoint pp){
super(pp.getCenterID(),atomicNo,pp.getCenter(), 1.0);
this.pp = pp;
}
public PPGaussian(PPGaussian original){
super(original.atomId,original.atomicNo,new Coordinates(original.center),original.weight);
this.pp = original.pp.copyPharmacophorePoint();
}
private PPGaussian(String encodedGaussian, StereoMolecule mol) {
decode(encodedGaussian,mol);
}
public static PPGaussian fromString(String encodedGaussian, StereoMolecule mol) {
return new PPGaussian(encodedGaussian, mol);
}
public Coordinates getRotatedDirectionality(double[][] rotMatrix, double scaleFactor) {
Coordinates directMod = pp.getRotatedDirectionality(rotMatrix,scaleFactor);
return directMod;
}
public double getVectorSimilarity(PPGaussian ppGauss2,Coordinates directionalityMod) {
return this.pp.getVectorSimilarity(ppGauss2.getPharmacophorePoint(),directionalityMod);
}
public double getVectorSimilarity(PPGaussian ppGauss2) {
return getVectorSimilarity(ppGauss2,ppGauss2.getPharmacophorePoint().getDirectionality());
}
public IPharmacophorePoint getPharmacophorePoint() {
return pp;
}
@Override
public void setAtomId(int atomID) {
this.pp.setCenterID(atomID);
}
@Override
public int getAtomId() {
return this.pp.getCenterID();
}
public double getSimilarity(PPGaussian ppGauss2, Coordinates directionality) {
double ppSimilarity = 1.0;
double vectorSim = getVectorSimilarity(ppGauss2,directionality);
double similarity = (Math.max(0, vectorSim)+2*ppSimilarity)/3.0;
return similarity;
}
public double getSimilarity(PPGaussian ppGauss2) {
return getSimilarity(ppGauss2, ppGauss2.getPharmacophorePoint().getDirectionality());
}
public double getInteractionSimilarity(PPGaussian ppGauss2) {
return pp.getSimilarity(ppGauss2.pp);
}
@Override
public void setCenter(Coordinates center) {
this.center = center;
this.pp.getCenter().x = center.x;
this.pp.getCenter().y = center.y;
this.pp.getCenter().z = center.z;
}
@Override
public String encode() { //encodes all information of an atomicGaussian using the Base64 encoder
Encoder encoder = Base64.getEncoder();
StringBuilder molVolString = new StringBuilder();
molVolString.append(Integer.toString(atomicNo));
molVolString.append(" ");
molVolString.append(encoder.encodeToString(EncodeFunctions.doubleToByteArray(weight)));
molVolString.append(" ");
molVolString.append(pp.encode());
return molVolString.toString();
}
public void decode(String string64, StereoMolecule mol) {
Decoder decoder = Base64.getDecoder();
String[] strings = string64.split(" ");
if(strings.length==1) { // no pharmacophore information encoded
return;
}
atomicNo = Integer.decode(strings[0]);
weight = EncodeFunctions.byteArrayToDouble(decoder.decode(strings[1].getBytes()));
StringBuilder sb = new StringBuilder();
for(int i=2;i